GenomicInteractions 1.0.3
Nathan Harmston
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GenomicInteractions | | Last Changed Rev: 96113 / Revision: 102249 | | Last Changed Date: 2014-10-28 07:08:47 -0700 (Tue, 28 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicInteractions_1.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GenomicInteractions.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicInteractions/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicInteractions’ version ‘1.0.3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicInteractions’ can be installed ... [22s/22s] OK
* checking installed package size ... NOTE
installed size is 10.7Mb
sub-directories of 1Mb or more:
doc 2.2Mb
extdata 7.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.importHicLib : .process.chr: no visible global function definition for
‘seqlengths’
.readBam: no visible global function definition for ‘seqlengths’
GenomicInteractions: no visible global function definition for
‘seqlengths’
plotCisTrans: no visible binding for global variable ‘category’
plotCisTrans: no visible binding for global variable ‘ymax’
plotCisTrans: no visible binding for global variable ‘ymin’
plotCisTrans: no visible binding for global variable ‘label’
plotCounts: no visible binding for global variable ‘Var1’
plotCounts: no visible binding for global variable ‘Freq’
plotDists: no visible binding for global variable ‘Distance’
plotInteractionAnnotations: no visible binding for global variable
‘fraction’
plotInteractionAnnotations: no visible binding for global variable
‘category’
plotInteractionAnnotations: no visible binding for global variable
‘ymax’
plotInteractionAnnotations: no visible binding for global variable
‘ymin’
plotInteractionAnnotations: no visible binding for global variable
‘label’
viewPoint: no visible global function definition for ‘seqlengths’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/25s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
GenomicInteractions-class 5.068 0.074 5.566
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
NOTE: There were 2 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/GenomicInteractions.Rcheck/00check.log’
for details.
* installing *source* package ‘GenomicInteractions’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘GenomicInteractions’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicInteractions)